Create your master branch:
$ cd project && cd project
$ git init
Create your files and commit:
$ git add .
$ git commit -m "First commit"
Now create gh-pages branch
git checkout --orphan gh-pages
git read-tree --prefix=_includes/ -u master
git commit -m "Master merged into gh-pages as subtree"
Work on your master branch as normal. Commit changes. When ready to push:
git checkout gh-pages
git merge -s subtree master --commit
git checkout master
Finally push
git push --all origin